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Syntax fixes for the JPA migrator

This commit is contained in:
James Agnew 2018-11-30 12:39:37 -05:00
parent 650872cd3e
commit b2179b1696
17 changed files with 109 additions and 39 deletions
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4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceReindexJobEntity.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/StaleSearchDeletingSvcImpl.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.search;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/IResourceReindexingSvc.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.search.reindex;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.search.reindex;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionInterceptor.java
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@ -68,9 +68,9 @@ import java.util.concurrent.*;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/ResourceModifiedMessage.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.subscription;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/JdbcUtils.java
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@ -127,7 +127,9 @@ public class JdbcUtils {
switch (dataType) {
case Types.VARCHAR:
return BaseTableColumnTypeTask.ColumnTypeEnum.STRING.getDescriptor(length);
case Types.NUMERIC:
case Types.BIGINT:
case Types.DECIMAL:
return BaseTableColumnTypeTask.ColumnTypeEnum.LONG.getDescriptor(null);
case Types.INTEGER:
return BaseTableColumnTypeTask.ColumnTypeEnum.INT.getDescriptor(null);
@ -135,7 +137,7 @@ public class JdbcUtils {
case Types.TIMESTAMP_WITH_TIMEZONE:
return BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMP.getDescriptor(null);
default:
throw new IllegalArgumentException("Don't know how to handle datatype: " + dataType);
throw new IllegalArgumentException("Don't know how to handle datatype " + dataType + " for column " + theColumnName + " on table " + theTableName);
}
}

4
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/Migrator.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

38
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ArbitrarySqlTask.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -42,6 +42,7 @@ public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
private List<Task> myTask = new ArrayList<>();
private int myBatchSize = 1000;
private String myExecuteOnlyIfTableExists;
private List<TableAndColumn> myConditionalOnExistenceOf = new ArrayList<>();
public ArbitrarySqlTask(String theTableName, String theDescription) {
myTableName = theTableName;
@ -69,6 +70,14 @@ public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
}
}
for (TableAndColumn next : myConditionalOnExistenceOf) {
String columnType = JdbcUtils.getColumnType(getConnectionProperties(), next.getTable(), next.getColumn());
if (columnType == null) {
ourLog.info("Table {} does not have column {} - No action performed", next.getTable(), next.getColumn());
return;
}
}
for (Task next : myTask) {
next.execute();
}
@ -83,6 +92,13 @@ public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
myExecuteOnlyIfTableExists = theExecuteOnlyIfTableExists;
}
/**
* This task will only execute if the following column exists
*/
public void addExecuteOnlyIfColumnExists(String theTableName, String theColumnName) {
myConditionalOnExistenceOf.add(new TableAndColumn(theTableName, theColumnName));
}
public enum QueryModeEnum {
BATCH_UNTIL_NO_MORE
}
@ -129,4 +145,22 @@ public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
} while (rows.size() > 0);
}
}
private static class TableAndColumn {
private final String myTable;
private final String myColumn;
private TableAndColumn(String theTable, String theColumn) {
myTable = theTable;
myColumn = theColumn;
}
public String getTable() {
return myTable;
}
public String getColumn() {
return myColumn;
}
}
}

4
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTask.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

25
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
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@ -36,7 +36,7 @@ import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
@SuppressWarnings({"UnstableApiUsage", "SqlNoDataSourceInspection", "SpellCheckingInspection"})
@SuppressWarnings({"SqlNoDataSourceInspection", "SpellCheckingInspection"})
public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
private final Set<FlagEnum> myFlags;
@ -90,10 +90,12 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
// Forced ID changes
Builder.BuilderWithTableName forcedId = version.onTable("HFJ_FORCED_ID");
version.startSectionWithMessage("Starting work on table: " + forcedId.getTableName());
forcedId
.dropIndex("IDX_FORCEDID_TYPE_FORCEDID");
forcedId
.dropIndex("IDX_FORCEDID_TYPE_RESID");
forcedId
.addIndex("IDX_FORCEDID_TYPE_FID")
.unique(true)
@ -332,9 +334,10 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
"from HFJ_RES_PARAM_PRESENT " +
"join HFJ_SEARCH_PARM ON (HFJ_SEARCH_PARM.PID = HFJ_RES_PARAM_PRESENT.SP_ID) " +
"where HFJ_RES_PARAM_PRESENT.HASH_PRESENCE is null";
consolidateSearchParamPresenceIndexesTask.addExecuteOnlyIfColumnExists("HFJ_RES_PARAM_PRESENT", "SP_ID");
consolidateSearchParamPresenceIndexesTask.addQuery(sql, ArbitrarySqlTask.QueryModeEnum.BATCH_UNTIL_NO_MORE, t -> {
Long pid = (Long) t.get("PID");
Boolean present = (Boolean) t.get("SP_PRESENT");
Number pid = (Number) t.get("PID");
Boolean present = columnToBoolean(t.get("SP_PRESENT"));
String resType = (String) t.get("RES_TYPE");
String paramName = (String) t.get("PARAM_NAME");
Long hash = SearchParamPresent.calculateHashPresence(resType, paramName, present);
@ -494,6 +497,18 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_MAP_GRP_ELM_TGT add constraint FK_TCMGETARGET_ELEMENT foreign key (CONCEPT_MAP_GRP_ELM_PID) references TRM_CONCEPT_MAP_GRP_ELEMENT");
}
private Boolean columnToBoolean(Object theValue) {
if (theValue == null) {
return null;
}
if (theValue instanceof Boolean) {
return (Boolean) theValue;
}
long longValue = ((Number) theValue).longValue();
return longValue == 1L;
}
private void init340() {
Builder version = forVersion(VersionEnum.V3_4_0);
@ -537,10 +552,6 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
myCommandLineValue = theCommandLineValue;
}
public String getCommandLineValue() {
return myCommandLineValue;
}
public static FlagEnum fromCommandLineValue(String theCommandLineValue) {
Optional<FlagEnum> retVal = Arrays.stream(values()).filter(t -> t.myCommandLineValue.equals(theCommandLineValue)).findFirst();
return retVal.orElseThrow(() -> {

13
hapi-fhir-jpaserver-uhnfhirtest/derby_maintenance.txt
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@ -121,6 +121,9 @@ drop table hfj_search_result cascade constraints;
drop table hfj_search_include cascade constraints;
drop table hfj_search cascade constraints;
drop table hfj_res_param_present cascade constraints;
DROP TABLE HFJ_RES_REINDEX_JOB cascade constraints;
DROP TABLE HFJ_SEARCH_PARM cascade constraints;
DROP TABLE HFJ_TAG_DEF cascade CONSTRAINTS;
drop table hfj_idx_cmp_string_uniq cascade constraints;
drop table hfj_subscription_stats cascade constraints;
drop table trm_concept_property cascade constraints;
@ -130,11 +133,11 @@ drop table trm_codesystem_ver cascade constraints;
drop table trm_codesystem cascade constraints;
DROP TABLE hfj_resource CASCADE CONSTRAINTS;
DROP TABLE hfj_res_ver CASCADE CONSTRAINTS;
drop table cdr_audit_evt_target_module cascade constraints;
drop table cdr_audit_evt_target_res cascade constraints;
drop table cdr_audit_evt_target_user cascade constraints;
drop table cdr_xact_log_step cascade constraints;
drop table cdr_xact_log cascade constraints;
DROP TABLE TRM_CONCEPT_DESIG CASCADE CONSTRAINTS;
DROP TABLE TRM_CONCEPT_MAP CASCADE CONSTRAINTS;
DROP TABLE TRM_CONCEPT_MAP_GROUP CASCADE CONSTRAINTS;
DROP TABLE TRM_CONCEPT_MAP_GRP_ELEMENT CASCADE CONSTRAINTS;
DROP TABLE TRM_CONCEPT_MAP_GRP_ELM_TGT CASCADE CONSTRAINTS;

4
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/BaseRule.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/IAuthRuleBuilderOperationNamed.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

20
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/IAuthRuleBuilderOperationNamedAndScoped.java
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@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.interceptor.auth;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2018 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
public interface IAuthRuleBuilderOperationNamedAndScoped {
/**

4
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/OperationRule.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.