Merge pull request #413 from ZihengSun/master

fix a few more issues

pom.xml

@@ -11,7 +11,7 @@
 	</parent>
 	<groupId>com.gw</groupId>
 	<artifactId>geoweaver</artifactId>
-	<version>1.1.1</version>
+	<version>1.2.1</version>
 	<name>geoweaver</name>
 	<description>A lightweight workflow management software for organizing data analysis workflows, 
 	preserving history of every workflow run, and improving scientist producitvity and workflow FAIRness,
@@ -173,7 +173,7 @@
 		<dependency>
 		    <groupId>org.json</groupId>
 		    <artifactId>json</artifactId>
-		    <version>20230227</version>
+		    <version>20231013</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>

src/main/java/com/gw/GeoweaverApplication.java

@@ -188,8 +188,6 @@ public static void addDefaultPublicUser(){
 
         }
 
-        logger.debug("test what is going on");
-
         //set everything that doesn't have an owner to this user
         ut.belongToPublicUser();
 

src/main/java/com/gw/database/EnvironmentRepository.java

@@ -7,22 +7,41 @@
 
 import com.gw.jpa.Environment;
 
-public interface EnvironmentRepository extends CrudRepository<Environment, String>{
-
-//	new StringBuffer("select * from environment where host = '").append(hostid)
-//	.append("' and bin = '").append(bin).append("' and pyenv = '")
-//	.append(env).append("' and basedir = '").append(basedir).append("';");
-	@Query(value = "select * from environment where hostid = ?1 and bin = ?2 and pyenv = ?3 and basedir = ?4 ",
-		nativeQuery = true)
-	Collection<Environment> findEnvByID_BIN_ENV_BaseDir(String hostid, String bin, String pyenv, String basedir);
-
-	@Query(value = "select * from environment where hostid = ?1 and bin = ?2",
-		nativeQuery = true)
-	Collection<Environment> findEnvByID_BIN(String hostid, String bin);
-
-
-	@Query(value = "select * from environment where hostid = ?1 ",
-		nativeQuery = true)
-	Collection<Environment> findEnvByHost(String hostid);
-
+/**
+ * The EnvironmentRepository interface provides methods for querying environment configurations from a database.
+ * It extends the CrudRepository interface to handle database operations for the Environment entity.
+ */
+public interface EnvironmentRepository extends CrudRepository<Environment, String> {
+
+    /**
+     * Find environment configurations based on the provided host ID, binary path, Python environment, and base directory.
+     *
+     * @param hostid   The ID of the host.
+     * @param bin      The binary path.
+     * @param pyenv    The Python environment.
+     * @param basedir  The base directory.
+     * @return A collection of environment configurations matching the specified criteria.
+     */
+    @Query(value = "select * from environment where hostid = ?1 and bin = ?2 and pyenv = ?3 and basedir = ?4", nativeQuery = true)
+    Collection<Environment> findEnvByID_BIN_ENV_BaseDir(String hostid, String bin, String pyenv, String basedir);
+
+    /**
+     * Find environment configurations based on the provided host ID and binary path.
+     *
+     * @param hostid The ID of the host.
+     * @param bin    The binary path.
+     * @return A collection of environment configurations matching the specified host and binary path.
+     */
+    @Query(value = "select * from environment where hostid = ?1 and bin = ?2", nativeQuery = true)
+    Collection<Environment> findEnvByID_BIN(String hostid, String bin);
+
+    /**
+     * Find environment configurations based on the provided host ID.
+     *
+     * @param hostid The ID of the host.
+     * @return A collection of environment configurations associated with the specified host.
+     */
+    @Query(value = "select * from environment where hostid = ?1", nativeQuery = true)
+    Collection<Environment> findEnvByHost(String hostid);
 }
+

src/main/java/com/gw/database/HistoryRepository.java

@@ -8,68 +8,129 @@
 
 import com.gw.jpa.History;
 
-public interface HistoryRepository extends JpaRepository<History, String>{
-
-	@Query(value="select * from history where host_id = ?1 ORDER BY history_begin_time DESC limit ?2",
-		nativeQuery = true)
-	Collection<History> findRecentHistory(String hostid, int limit);
-
-	@Query(value="select * from history where indicator='Running'  ORDER BY history_begin_time DESC;",
-		nativeQuery = true)
-	List<History> findAllRunningResource();
-
-	@Query(value="select * from history, workflow where history.history_process = workflow.id and history.indicator = 'Running' ORDER BY history_begin_time DESC;",
-		nativeQuery = true)
-	List<Object[]> findRunningWorkflow();
-
-	@Query(value="select * from history, workflow where history.history_process = workflow.id and history.indicator = 'Failed' ORDER BY history_begin_time DESC;",
-		nativeQuery = true)
-	List<Object[]> findFailedWorkflow();
-
-	@Query(value="select * from history, workflow where history.history_process = workflow.id and history.indicator = 'Done' ORDER BY history_begin_time DESC;",
-		nativeQuery = true)
-	List<Object[]> findSuccessWorkflow();
-
-	@Query(value="select * from history, gwprocess where history.history_process = gwprocess.id and history.indicator = 'Running' ORDER BY history_begin_time DESC;",
-		nativeQuery = true)
-	List<Object[]> findRunningProcess();
-
-	@Query(value="select * from history, gwprocess where history.history_process = gwprocess.id and history.indicator = 'Failed' ORDER BY history_begin_time DESC;",
-		nativeQuery = true)
-	List<Object[]> findFailedProcess();
-
-	@Query(value="select * from history, gwprocess where history.history_process = gwprocess.id and history.indicator = 'Done' ORDER BY history_begin_time DESC;",
-		nativeQuery = true)
-	List<Object[]> findSuccessProcess();
-
-	@Query(value="select * from history where history.history_process = ?1 ORDER BY history_begin_time DESC;",
-			nativeQuery = true)
-	List<History> findByProcessId(String pid);
-
-	@Query(value="select * from history where history.history_process = ?1 and history.indicator != 'Skipped' ORDER BY history_begin_time DESC;",
-			nativeQuery = true)
-	List<History> findByProcessIdIgnoreUnknown(String pid);
-
-	@Query(value="select * from history where history.history_process = ?1 ORDER BY history_begin_time DESC;",
-			nativeQuery = true)
-	List<History> findByWorkflowId(String wid);
-
-
-	@Query(value="select * from history, workflow where workflow.id = history.history_process ORDER BY history_begin_time DESC limit ?1",
-		nativeQuery = true)
-	List<Object[]> findRecentWorkflow(int limit);
-
-
-	@Query(value="select * from history, gwprocess where gwprocess.id = history.history_process ORDER BY history_begin_time DESC limit ?1",
-		nativeQuery = true)
-	List<Object[]> findRecentProcess(int limit);
-
-	@Query(value="select * from history, gwprocess where history.history_id = ?1 and history.history_process=gwprocess.id",
-		nativeQuery = true)
-	List<Object[]> findOneHistoryofProcess(String history_id);
-
-
-
-
-
+/**
+ * The HistoryRepository interface provides methods for querying historical execution data (history) from a database.
+ * It extends the JpaRepository interface to handle database operations.
+ */
+public interface HistoryRepository extends JpaRepository<History, String> {
+
+    /**
+     * Find recent history records for a specific host, limited by the specified count.
+     *
+     * @param hostid The ID of the host.
+     * @param limit  The maximum number of history records to retrieve.
+     * @return A collection of recent history records for the host.
+     */
+    @Query(value = "select * from history where host_id = ?1 ORDER BY history_begin_time DESC limit ?2", nativeQuery = true)
+    Collection<History> findRecentHistory(String hostid, int limit);
+
+    /**
+     * Find all running history records.
+     *
+     * @return A list of all running history records.
+     */
+    @Query(value = "select * from history where indicator='Running'  ORDER BY history_begin_time DESC;", nativeQuery = true)
+    List<History> findAllRunningResource();
+
+    /**
+     * Find all running workflows.
+     *
+     * @return A list of all running workflow records with additional information.
+     */
+    @Query(value = "select * from history, workflow where history.history_process = workflow.id and history.indicator = 'Running' ORDER BY history_begin_time DESC;", nativeQuery = true)
+    List<Object[]> findRunningWorkflow();
+
+    /**
+     * Find all failed workflows.
+     *
+     * @return A list of all failed workflow records with additional information.
+     */
+    @Query(value = "select * from history, workflow where history.history_process = workflow.id and history.indicator = 'Failed' ORDER BY history_begin_time DESC;", nativeQuery = true)
+    List<Object[]> findFailedWorkflow();
+
+    /**
+     * Find all successfully completed workflows.
+     *
+     * @return A list of all successful workflow records with additional information.
+     */
+    @Query(value = "select * from history, workflow where history.history_process = workflow.id and history.indicator = 'Done' ORDER BY history_begin_time DESC;", nativeQuery = true)
+    List<Object[]> findSuccessWorkflow();
+
+    /**
+     * Find all running processes.
+     *
+     * @return A list of all running process records with additional information.
+     */
+    @Query(value = "select * from history, gwprocess where history.history_process = gwprocess.id and history.indicator = 'Running' ORDER BY history_begin_time DESC;", nativeQuery = true)
+    List<Object[]> findRunningProcess();
+
+    /**
+     * Find all failed processes.
+     *
+     * @return A list of all failed process records with additional information.
+     */
+    @Query(value = "select * from history, gwprocess where history.history_process = gwprocess.id and history.indicator = 'Failed' ORDER BY history_begin_time DESC;", nativeQuery = true)
+    List<Object[]> findFailedProcess();
+
+    /**
+     * Find all successfully completed processes.
+     *
+     * @return A list of all successful process records with additional information.
+     */
+    @Query(value = "select * from history, gwprocess where history.history_process = gwprocess.id and history.indicator = 'Done' ORDER BY history_begin_time DESC;", nativeQuery = true)
+    List<Object[]> findSuccessProcess();
+
+    /**
+     * Find history records by process ID.
+     *
+     * @param pid The ID of the process.
+     * @return A list of history records associated with the specified process ID.
+     */
+    @Query(value = "select * from history where history.history_process = ?1 ORDER BY history_begin_time DESC;", nativeQuery = true)
+    List<History> findByProcessId(String pid);
+
+    /**
+     * Find history records by process ID, excluding 'Skipped' indicator.
+     *
+     * @param pid The ID of the process.
+     * @return A list of history records associated with the specified process ID, excluding 'Skipped' records.
+     */
+    @Query(value = "select * from history where history.history_process = ?1 and history.indicator != 'Skipped' ORDER BY history_begin_time DESC;", nativeQuery = true)
+    List<History> findByProcessIdIgnoreUnknown(String pid);
+
+    /**
+     * Find history records by workflow ID.
+     *
+     * @param wid The ID of the workflow.
+     * @return A list of history records associated with the specified workflow ID.
+     */
+    @Query(value = "select * from history where history.history_process = ?1 ORDER BY history_begin_time DESC;", nativeQuery = true)
+    List<History> findByWorkflowId(String wid);
+
+    /**
+     * Find recent workflow records, limited by the specified count.
+     *
+     * @param limit The maximum number of recent workflow records to retrieve.
+     * @return A list of recent workflow records with additional information.
+     */
+    @Query(value = "select * from history, workflow where workflow.id = history.history_process ORDER BY history_begin_time DESC limit ?1", nativeQuery = true)
+    List<Object[]> findRecentWorkflow(int limit);
+
+    /**
+     * Find recent process records, limited by the specified count.
+     *
+     * @param limit The maximum number of recent process records to retrieve.
+     * @return A list of recent process records with additional information.
+     */
+    @Query(value = "select * from history, gwprocess where gwprocess.id = history.history_process ORDER BY history_begin_time DESC limit ?1", nativeQuery = true)
+    List<Object[]> findRecentProcess(int limit);
+
+    /**
+     * Find a history record associated with a specific history ID.
+     *
+     * @param history_id The ID of the history record.
+     * @return A list containing a history record and additional information about the associated process.
+     */
+    @Query(value = "select * from history, gwprocess where history.history_id = ?1 and history.history_process=gwprocess.id", nativeQuery = true)
+    List<Object[]> findOneHistoryofProcess(String history_id);
 }