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[issue-2408] Migrated JDBC Google BigQuery driver to v1.6.1.1002 #2

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[issue-2408] Migrated JDBC Google BigQuery driver to v1.6.1.1002 #2

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bc73067
Remove the wild card permissions from the CohortCharacterizationPermi…
chrisknoll Nov 22, 2024
fce763f
[issue-2379][issue-2408] Migrated JDBC Snowflake driver to v3.20.0 (#…
oleg-odysseus Nov 26, 2024
e41dc29
Removed dependency on commons lang (#2415)
chrisknoll Nov 27, 2024
e7e6055
Add endpoint to clear the cdm_cache and achilles_cache (#2406)
amarsan Nov 27, 2024
02a9c9f
Add handling for Snowflake IN clause limit (#2404)
anthonysena Dec 3, 2024
67f8816
Extending Concept Set Items with Annotations (#2403)
alex-odysseus Dec 17, 2024
70dc4e2
Re-introduce Caching (#2393)
chrisknoll Dec 17, 2024
c2d6c4a
[issue-2408] Migrated JDBC Google BigQuery driver to v1.6.1.1002
oleg-odysseus Nov 22, 2024
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12 changes: 12 additions & 0 deletions .editorconfig
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
# EditorConfig is awesome: https://EditorConfig.org

# top-most EditorConfig file
root = true

[*]
indent_style = tab
indent_size = 2
end_of_line = crlf
charset = utf-8
trim_trailing_whitespace = false
insert_final_newline = false
131 changes: 76 additions & 55 deletions pom.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">

<modelVersion>4.0.0</modelVersion>

Expand Down Expand Up @@ -122,7 +122,7 @@
<security.ad.system.password></security.ad.system.password>
<security.ad.searchFilter>(&amp;(objectClass=person)(cn=%s))</security.ad.searchFilter>
<security.ad.ignore.partial.result.exception>true</security.ad.ignore.partial.result.exception>
<security.ad.result.count.limit>30000</security.ad.result.count.limit> <!-- 0 means no limit -->
<security.ad.result.count.limit>30000</security.ad.result.count.limit> <!-- 0 means no limit -->
<security.ad.default.import.group>public</security.ad.default.import.group>
<security.ad.searchString>(&amp;(objectClass=person)(userPrincipalName=%s))</security.ad.searchString>
<security.ad.userMapping.displaynameAttr>displayname</security.ad.userMapping.displaynameAttr>
Expand Down Expand Up @@ -191,8 +191,8 @@
<!-- If defaultGlobalReadPermissions is set to true (default), then all users can see every artifact. -->
<!-- If it is set to false, WebAPI will filter out the artifacts that a user does not explicitly have -->
<!-- read permissions to -->
<security.defaultGlobalReadPermissions>true</security.defaultGlobalReadPermissions>
<security.defaultGlobalReadPermissions>true</security.defaultGlobalReadPermissions>

<!-- EMBEDDED SERVER CONFIGURATION (ServerProperties) -->
<server.port>8080</server.port>
<server.ssl.key-store></server.ssl.key-store>
Expand All @@ -216,7 +216,7 @@
<jasypt.encryptor.enabled>false</jasypt.encryptor.enabled>
<jasypt.encryptor.password></jasypt.encryptor.password>
<jasypt.encryptor.algorithm>PBEWithMD5AndDES</jasypt.encryptor.algorithm>

<!-- ORGANIZATION SETTINGS -->
<organization.name>OHDSI</organization.name>

Expand All @@ -236,6 +236,10 @@
<logging.level.org.hibernate>info</logging.level.org.hibernate>
<logging.level.org.apache.shiro>warn</logging.level.org.apache.shiro>

<!-- Spring Cache properties -->
<spring.cache.type>jcache</spring.cache.type>

<!-- Spring Batch -->
<spring.batch.taskExecutor.corePoolSize>10</spring.batch.taskExecutor.corePoolSize>
<spring.batch.taskExecutor.maxPoolSize>20</spring.batch.taskExecutor.maxPoolSize>
<spring.batch.taskExecutor.queueCapacity>2147483647</spring.batch.taskExecutor.queueCapacity>
Expand Down Expand Up @@ -272,6 +276,7 @@
<cache.jobs.count>3</cache.jobs.count>
<!-- Achilles cache -->
<cache.achilles.usePersonCount>true</cache.achilles.usePersonCount>
<cache.webapi.enabled>true</cache.webapi.enabled>

<!-- Build info -->
<buildinfo.atlas.milestone.id>47</buildinfo.atlas.milestone.id>
Expand All @@ -298,6 +303,7 @@
<audit.trail.log.file>/tmp/atlas/audit/audit.log</audit.trail.log.file>
<audit.trail.log.extraFile>/tmp/atlas/audit/audit-extra.log</audit.trail.log.extraFile>
</properties>

<build>
<finalName>WebAPI</finalName>
<sourceDirectory>${basedir}/src/main/java</sourceDirectory>
Expand Down Expand Up @@ -368,8 +374,8 @@
<!-- only include properties to speed up plugin -->
<!-- ref: https://github.com/git-commit-id/git-commit-id-maven-plugin/issues/462 -->
<includeOnlyProperties>
<includeOnlyProperty>git.branch</includeOnlyProperty>
<includeOnlyProperty>git.commit.id.abbrev</includeOnlyProperty>
<includeOnlyProperty>git.branch</includeOnlyProperty>
<includeOnlyProperty>git.commit.id.abbrev</includeOnlyProperty>
</includeOnlyProperties>
</configuration>
</plugin>
Expand Down Expand Up @@ -575,6 +581,7 @@
</dependency>
</dependencies>
</dependencyManagement>

<dependencies>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
Expand Down Expand Up @@ -742,6 +749,10 @@
<scope>provided</scope>
</dependency>
<dependency>
<groupId>javax.cache</groupId>
<artifactId>cache-api</artifactId>
<version>1.1.1</version>
</dependency> <dependency>
<groupId>org.ohdsi.sql</groupId>
<artifactId>SqlRender</artifactId>
<version>${SqlRender.version}</version>
Expand Down Expand Up @@ -780,6 +791,11 @@
<artifactId>commons-lang3</artifactId>
<version>3.12.0</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>1.10.0</version>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
Expand Down Expand Up @@ -808,12 +824,12 @@
<artifactId>jackson-databind</artifactId>
</exclusion>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
</exclusion>
<exclusion>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</exclusion>
</exclusions>
</dependency>
Expand Down Expand Up @@ -1159,7 +1175,7 @@
<version>${pac4j.version}</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
</exclusions>
Expand Down Expand Up @@ -1195,6 +1211,10 @@
<version>1.1.7</version>
</dependency>
<dependency>
<groupId>org.ehcache</groupId>
<artifactId>ehcache</artifactId>
<version>3.9.11</version>
</dependency> <dependency>
<groupId>com.opentable.components</groupId>
<artifactId>otj-pg-embedded</artifactId>
<version>0.13.1</version>
Expand All @@ -1205,12 +1225,12 @@
<artifactId>spring-boot-starter-test</artifactId>
<version>${spring.boot.version}</version>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>com.vaadin.external.google</groupId>
<artifactId>android-json</artifactId>
</exclusion>
</exclusions>
<exclusions>
<exclusion>
<groupId>com.vaadin.external.google</groupId>
<artifactId>android-json</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.dbunit</groupId>
Expand All @@ -1231,12 +1251,13 @@
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.github.mjeanroy</groupId>
<artifactId>dbunit-plus</artifactId>
<version>2.0.1</version>
<scope>test</scope>
<groupId>com.github.mjeanroy</groupId>
<artifactId>dbunit-plus</artifactId>
<version>2.0.1</version>
<scope>test</scope>
</dependency>
</dependencies>

<profiles>
<profile>
<id>webapi-oracle</id>
Expand Down Expand Up @@ -1329,17 +1350,17 @@
lower(email) = lower(?)</security.db.datasource.authenticationQuery>
</properties>
<repositories>
<repository>
<repository>
<id>ohdsi.snapshots</id>
<name>repo.ohdsi.org-snapshots</name>
<url>https://repo.ohdsi.org/nexus/content/repositories/snapshots</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
</snapshots>
</repository>
</repositories>
</profile>
<profile>
Expand Down Expand Up @@ -1412,7 +1433,7 @@
<impala.enabled>true</impala.enabled>
<impala.driver.version>2.6.15</impala.driver.version>
<!-- Impala JDBC driver path -->
<impala.classpath>...path/to/impala/jdbc/drivers...</impala.classpath>
<impala.classpath>...path/to/impala/jdbc/drivers...</impala.classpath>
</properties>
<dependencies>
<dependency>
Expand Down Expand Up @@ -1509,67 +1530,67 @@
<dependency>
<groupId>com.google.api-client</groupId>
<artifactId>google-api-client</artifactId>
<version>1.33.4</version>
<version>2.3.0</version>
</dependency>
<dependency>
<groupId>com.google.apis</groupId>
<artifactId>google-api-services-bigquery</artifactId>
<version>v2-rev20220326-1.32.1</version>
<version>v2-rev20240211-2.0.0</version>
</dependency>
<dependency>
<groupId>com.google.cloud</groupId>
<artifactId>google-cloud-bigquery</artifactId>
<version>1.2.15</version>
<version>1.6.1.1002</version>
</dependency>
<dependency>
<groupId>com.google.http-client</groupId>
<artifactId>google-http-client</artifactId>
<version>1.41.5</version>
<version>1.44.1</version>
</dependency>
<dependency>
<groupId>com.google.http-client</groupId>
<artifactId>google-http-client-gson</artifactId>
<version>1.41.5</version>
<version>1.44.1</version>
</dependency>
<dependency>
<groupId>com.google.oauth-client</groupId>
<artifactId>google-oauth-client</artifactId>
<version>1.33.3</version>
<version>1.35.0</version>
</dependency>
<dependency>
<groupId>com.google.cloud</groupId>
<artifactId>google-cloud-bigquerystorage</artifactId>
<version>2.12.0</version>
<version>3.2.0</version>
</dependency>
<dependency>
<groupId>com.google.auth</groupId>
<artifactId>google-auth-library-oauth2-http</artifactId>
<version>1.6.0</version>
<version>1.23.0</version>
</dependency>
<dependency>
<groupId>com.google.auth</groupId>
<artifactId>google-auth-library-credentials</artifactId>
<version>1.6.0</version>
<version>1.23.0</version>
</dependency>
<dependency>
<groupId>com.google.api</groupId>
<artifactId>gax</artifactId>
<version>2.13.0</version>
<version>2.43.0</version>
</dependency>
<dependency>
<groupId>com.google.api</groupId>
<artifactId>gax-grpc</artifactId>
<version>2.13.0</version>
<version>2.43.0</version>
</dependency>
<dependency>
<groupId>com.google.api.grpc</groupId>
<artifactId>proto-google-cloud-bigquerystorage-v1</artifactId>
<version>2.12.0</version>
<version>3.2.0</version>
</dependency>
<dependency>
<groupId>io.opencensus</groupId>
<artifactId>opencensus-contrib-http-util</artifactId>
<version>0.31.0</version>
<version>0.31.1</version>
</dependency>
</dependencies>
<build>
Expand All @@ -1588,9 +1609,9 @@
<configuration>
<groupId>com.google.api-client</groupId>
<artifactId>google-api-client</artifactId>
<version>1.33.4</version>
<version>2.3.0</version>
<packaging>jar</packaging>
<file>${bigquery.classpath}/google-api-client-1.33.4.jar</file>
<file>${bigquery.classpath}/google-api-client-2.3.0.jar</file>
</configuration>
</execution>
<execution>
Expand All @@ -1602,9 +1623,9 @@
<configuration>
<groupId>com.google.apis</groupId>
<artifactId>google-api-services-bigquery</artifactId>
<version>v2-rev20220326-1.32.1</version>
<version>v2-rev20240211-2.0.0</version>
<packaging>jar</packaging>
<file>${bigquery.classpath}/google-api-services-bigquery-v2-rev20220326-1.32.1.jar</file>
<file>${bigquery.classpath}/google-api-services-bigquery-v2-rev20240211-2.0.0.jar</file>
</configuration>
</execution>
<execution>
Expand All @@ -1616,7 +1637,7 @@
<configuration>
<groupId>com.google.cloud</groupId>
<artifactId>google-cloud-bigquery</artifactId>
<version>1.2.15</version>
<version>1.6.1.1002</version>
<packaging>jar</packaging>
<file>${bigquery.classpath}/GoogleBigQueryJDBC42.jar</file>
</configuration>
Expand All @@ -1630,9 +1651,9 @@
<configuration>
<groupId>com.google.http-client</groupId>
<artifactId>google-http-client</artifactId>
<version>1.41.5</version>
<version>1.44.1</version>
<packaging>jar</packaging>
<file>${bigquery.classpath}/google-http-client-1.41.5.jar</file>
<file>${bigquery.classpath}/google-http-client-1.44.1.jar</file>
</configuration>
</execution>
<execution>
Expand All @@ -1644,9 +1665,9 @@
<configuration>
<groupId>com.google.http-client</groupId>
<artifactId>google-http-client-gson</artifactId>
<version>1.41.5</version>
<version>1.44.1</version>
<packaging>jar</packaging>
<file>${bigquery.classpath}/google-http-client-gson-1.41.5.jar</file>
<file>${bigquery.classpath}/google-http-client-gson-1.44.1.jar</file>
</configuration>
</execution>
<execution>
Expand All @@ -1658,9 +1679,9 @@
<configuration>
<groupId>com.google.oauth-client</groupId>
<artifactId>google-oauth-client</artifactId>
<version>1.33.1</version>
<version>1.35.0</version>
<packaging>jar</packaging>
<file>${bigquery.classpath}/google-oauth-client-1.33.1.jar</file>
<file>${bigquery.classpath}/google-oauth-client-1.35.0.jar</file>
</configuration>
</execution>
<execution>
Expand All @@ -1672,9 +1693,9 @@
<configuration>
<groupId>com.google.cloud</groupId>
<artifactId>google-cloud-bigquerystorage</artifactId>
<version>2.12.0</version>
<version>3.2.0</version>
<packaging>jar</packaging>
<file>${bigquery.classpath}/google-cloud-bigquerystorage-2.12.0.jar</file>
<file>${bigquery.classpath}/google-cloud-bigquerystorage-3.2.0.jar</file>
</configuration>
</execution>
</executions>
Expand Down Expand Up @@ -1828,7 +1849,7 @@
<id>webapi-snowflake</id>
<properties>
<snowflake.enabled>true</snowflake.enabled>
<snowflake.driver.version>3.13.22</snowflake.driver.version>
<snowflake.driver.version>3.20.0</snowflake.driver.version>
</properties>
<dependencies>
<dependency>
Expand Down
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