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Fixes/fix db schema #90

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merged 7 commits into from
Oct 3, 2023
Merged

Fixes/fix db schema #90

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ffacdeb
Change from VARCHAR to TEXT to work with mysql
seppinho Mar 10, 2023
030cc10
Delete empty block
seppinho Mar 10, 2023
905af0f
Revert empty block deletion
seppinho Jul 20, 2023
ed1ad96
Migrate genepi-db classes
seppinho Jul 20, 2023
c9b892e
Fix empty SQL block execution
seppinho Jul 20, 2023
0874503
Fix issue with non-unique schemas
seppinho Jul 20, 2023
f2e4377
Merge branch 'master' into fixes/fix-db-schema
seppinho Oct 3, 2023
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3 changes: 3 additions & 0 deletions .settings/org.eclipse.jdt.core.prefs
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eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
22 changes: 10 additions & 12 deletions pom.xml
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Expand Up @@ -94,19 +94,17 @@
</exclusion>
</exclusions>
</dependency>

<dependency>
<groupId>genepi</groupId>
<artifactId>genepi-db</artifactId>
<version>1.2.1</version>
<exclusions>
<exclusion>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</exclusion>
</exclusions>
</dependency>

<groupId>commons-dbutils</groupId>
<artifactId>commons-dbutils</artifactId>
<version>1.7</version>
</dependency>

<dependency>
<groupId>commons-dbcp</groupId>
<artifactId>commons-dbcp</artifactId>
<version>1.4</version>
</dependency>
<dependency>
<groupId>genepi</groupId>
<artifactId>genepi-hadoop</artifactId>
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6 changes: 3 additions & 3 deletions src/main/java/cloudgene/mapred/Main.java
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import com.esotericsoftware.yamlbeans.YamlReader;

import cloudgene.mapred.database.updates.BcryptHashUpdate;
import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.database.util.DatabaseConnector;
import cloudgene.mapred.database.util.DatabaseConnectorFactory;
import cloudgene.mapred.database.util.DatabaseUpdater;
import cloudgene.mapred.database.util.Fixtures;
import cloudgene.mapred.jobs.PersistentWorkflowEngine;
import cloudgene.mapred.jobs.WorkflowEngine;
import cloudgene.mapred.plugins.PluginManager;
import cloudgene.mapred.util.BuildUtil;
import cloudgene.mapred.util.Config;
import cloudgene.mapred.util.Settings;
import genepi.db.Database;
import genepi.db.DatabaseConnector;
import genepi.db.DatabaseUpdater;
import genepi.io.FileUtil;

public class Main {
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3 changes: 1 addition & 2 deletions src/main/java/cloudgene/mapred/WebApp.java
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import cloudgene.mapred.api.v2.users.UpdatePassword;
import cloudgene.mapred.api.v2.users.UserProfile;
import cloudgene.mapred.api.v2.users.VerifyApiToken;
import cloudgene.mapred.apps.ApplicationRepository;
import cloudgene.mapred.database.TemplateDao;
import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.jobs.WorkflowEngine;
import cloudgene.mapred.representations.CustomStatusService;
import cloudgene.mapred.resources.Admin;
import cloudgene.mapred.resources.Index;
import cloudgene.mapred.resources.Start;
import cloudgene.mapred.util.Settings;
import genepi.db.Database;

public class WebApp extends Application {

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3 changes: 1 addition & 2 deletions src/main/java/cloudgene/mapred/WebServer.java
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Expand Up @@ -8,11 +8,10 @@
import org.restlet.data.Protocol;
import org.restlet.routing.VirtualHost;

import cloudgene.mapred.apps.Application;
import cloudgene.mapred.cron.CronJobScheduler;
import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.jobs.WorkflowEngine;
import cloudgene.mapred.util.Settings;
import genepi.db.Database;

public class WebServer extends Component {

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2 changes: 0 additions & 2 deletions src/main/java/cloudgene/mapred/api/v2/jobs/NextflowWebLog.java
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package cloudgene.mapred.api.v2.jobs;

import java.io.IOException;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.restlet.representation.Representation;
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6 changes: 1 addition & 5 deletions src/main/java/cloudgene/mapred/apps/ApplicationRepository.java
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@@ -1,8 +1,6 @@
package cloudgene.mapred.apps;

import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
Expand All @@ -18,15 +16,13 @@

import com.amazonaws.services.s3.model.ObjectListing;
import com.amazonaws.services.s3.model.S3ObjectSummary;
import com.esotericsoftware.yamlbeans.YamlReader;
import com.esotericsoftware.yamlbeans.YamlWriter;

import cloudgene.mapred.core.User;
import cloudgene.mapred.database.util.DatabaseUpdater;
import cloudgene.mapred.util.GitHubException;
import cloudgene.mapred.util.GitHubUtil;
import cloudgene.mapred.util.GitHubUtil.Repository;
import cloudgene.mapred.wdl.WdlApp;
import genepi.db.DatabaseUpdater;
import genepi.hadoop.S3Util;
import genepi.io.FileUtil;
import net.lingala.zip4j.ZipFile;
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2 changes: 1 addition & 1 deletion src/main/java/cloudgene/mapred/core/ApiTokenVerifier.java
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import com.nimbusds.jose.crypto.MACVerifier;

import cloudgene.mapred.database.UserDao;
import genepi.db.Database;
import cloudgene.mapred.database.util.Database;

public class ApiTokenVerifier {

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2 changes: 1 addition & 1 deletion src/main/java/cloudgene/mapred/core/JWTUtil.java
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import org.restlet.util.Series;

import cloudgene.mapred.database.UserDao;
import genepi.db.Database;
import cloudgene.mapred.database.util.Database;

public class JWTUtil {

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2 changes: 1 addition & 1 deletion src/main/java/cloudgene/mapred/cron/CleanUpTasks.java
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import cloudgene.mapred.WebApp;
import cloudgene.mapred.database.JobDao;
import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.jobs.AbstractJob;
import cloudgene.mapred.jobs.workspace.ExternalWorkspaceFactory;
import cloudgene.mapred.util.MailUtil;
import cloudgene.mapred.util.Settings;
import cloudgene.mapred.util.Template;
import cloudgene.sdk.internal.IExternalWorkspace;
import genepi.db.Database;
import genepi.hadoop.HdfsUtil;
import genepi.io.FileUtil;

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2 changes: 1 addition & 1 deletion src/main/java/cloudgene/mapred/cron/RetireJob.java
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import org.quartz.JobExecutionException;

import cloudgene.mapred.WebApp;
import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.util.Settings;
import genepi.db.Database;

public class RetireJob implements Job {

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2 changes: 1 addition & 1 deletion src/main/java/cloudgene/mapred/cron/StatisticsJob.java
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import cloudgene.mapred.core.User;
import cloudgene.mapred.database.CounterHistoryDao;
import cloudgene.mapred.database.UserDao;
import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.jobs.AbstractJob;
import cloudgene.mapred.jobs.WorkflowEngine;
import genepi.db.Database;

public class StatisticsJob implements Job {

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6 changes: 3 additions & 3 deletions src/main/java/cloudgene/mapred/database/CounterDao.java
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import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.database.util.IRowMapMapper;
import cloudgene.mapred.database.util.JdbcDataAccessObject;
import cloudgene.mapred.jobs.AbstractJob;
import genepi.db.Database;
import genepi.db.IRowMapMapper;
import genepi.db.JdbcDataAccessObject;

public class CounterDao extends JdbcDataAccessObject {

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4 changes: 2 additions & 2 deletions src/main/java/cloudgene/mapred/database/CounterHistoryDao.java
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Expand Up @@ -14,8 +14,8 @@
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import genepi.db.Database;
import genepi.db.JdbcDataAccessObject;
import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.database.util.JdbcDataAccessObject;

public class CounterHistoryDao extends JdbcDataAccessObject {

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6 changes: 3 additions & 3 deletions src/main/java/cloudgene/mapred/database/DownloadDao.java
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import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.database.util.IRowMapper;
import cloudgene.mapred.database.util.JdbcDataAccessObject;
import cloudgene.mapred.jobs.CloudgeneParameterOutput;
import cloudgene.mapred.jobs.Download;
import genepi.db.Database;
import genepi.db.IRowMapper;
import genepi.db.JdbcDataAccessObject;

public class DownloadDao extends JdbcDataAccessObject {

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7 changes: 4 additions & 3 deletions src/main/java/cloudgene/mapred/database/JobDao.java
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import cloudgene.mapred.core.User;
import cloudgene.mapred.database.UserDao.UserMapper;
import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.database.util.IRowMapper;
import cloudgene.mapred.database.util.JdbcDataAccessObject;
import cloudgene.mapred.database.util.JdbcDataAccessObject.IntegerMapper;
import cloudgene.mapred.jobs.AbstractJob;
import cloudgene.mapred.jobs.CloudgeneJob;
import cloudgene.mapred.jobs.CloudgeneParameterInput;
import cloudgene.mapred.jobs.CloudgeneParameterOutput;
import cloudgene.mapred.jobs.CloudgeneStep;
import genepi.db.Database;
import genepi.db.IRowMapper;
import genepi.db.JdbcDataAccessObject;

public class JobDao extends JdbcDataAccessObject {

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6 changes: 3 additions & 3 deletions src/main/java/cloudgene/mapred/database/MessageDao.java
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import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.database.util.IRowMapper;
import cloudgene.mapred.database.util.JdbcDataAccessObject;
import cloudgene.mapred.jobs.CloudgeneStep;
import cloudgene.mapred.jobs.Message;
import genepi.db.Database;
import genepi.db.IRowMapper;
import genepi.db.JdbcDataAccessObject;

public class MessageDao extends JdbcDataAccessObject {

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6 changes: 3 additions & 3 deletions src/main/java/cloudgene/mapred/database/ParameterDao.java
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import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.database.util.IRowMapper;
import cloudgene.mapred.database.util.JdbcDataAccessObject;
import cloudgene.mapred.jobs.AbstractJob;
import cloudgene.mapred.jobs.CloudgeneParameterInput;
import cloudgene.mapred.jobs.CloudgeneParameterOutput;
import cloudgene.mapred.jobs.Download;
import cloudgene.mapred.wdl.WdlParameterInputType;
import cloudgene.mapred.wdl.WdlParameterOutputType;
import genepi.db.Database;
import genepi.db.IRowMapper;
import genepi.db.JdbcDataAccessObject;

public class ParameterDao extends JdbcDataAccessObject {

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6 changes: 3 additions & 3 deletions src/main/java/cloudgene/mapred/database/StepDao.java
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import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.database.util.IRowMapper;
import cloudgene.mapred.database.util.JdbcDataAccessObject;
import cloudgene.mapred.jobs.CloudgeneJob;
import cloudgene.mapred.jobs.CloudgeneStep;
import cloudgene.mapred.jobs.Message;
import cloudgene.mapred.steps.EmptyStep;
import genepi.db.Database;
import genepi.db.IRowMapper;
import genepi.db.JdbcDataAccessObject;

public class StepDao extends JdbcDataAccessObject {

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6 changes: 3 additions & 3 deletions src/main/java/cloudgene/mapred/database/TemplateDao.java
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import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.database.util.IRowMapper;
import cloudgene.mapred.database.util.JdbcDataAccessObject;
import cloudgene.mapred.util.Template;
import genepi.db.Database;
import genepi.db.IRowMapper;
import genepi.db.JdbcDataAccessObject;

public class TemplateDao extends JdbcDataAccessObject {

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6 changes: 3 additions & 3 deletions src/main/java/cloudgene/mapred/database/UserDao.java
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Expand Up @@ -9,10 +9,10 @@
import org.apache.commons.logging.LogFactory;

import cloudgene.mapred.core.User;
import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.database.util.IRowMapper;
import cloudgene.mapred.database.util.JdbcDataAccessObject;
import cloudgene.mapred.util.PublicUser;
import genepi.db.Database;
import genepi.db.IRowMapper;
import genepi.db.JdbcDataAccessObject;

public class UserDao extends JdbcDataAccessObject {

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4 changes: 2 additions & 2 deletions src/main/java/cloudgene/mapred/database/updates/BcryptHashUpdate.java
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import cloudgene.mapred.core.User;
import cloudgene.mapred.database.UserDao;
import genepi.db.Database;
import genepi.db.IUpdateListener;
import cloudgene.mapred.database.util.Database;
import cloudgene.mapred.database.util.IUpdateListener;

public class BcryptHashUpdate implements IUpdateListener {

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