#1999

Committed 13 May 2026 10:23PM UTC coverage: 70.05% (-0.3%) from 70.334%

Build # #1999

Build Type

Pull #751

github

Committed by

kinow

Commit Message

Last fixes to ease working with the SPARQL queries for a future PR, and more string concatenation removal

Pull Request Pull Request #751: Bump org.springframework.boot:spring-boot-starter-parent from 3.1.4 to 4.1.0-RC1

Coverage Stats

120 of 208 new or added lines in 30 files covered. (57.69%)

21 existing lines in 5 files now uncovered.

1691 of 2414 relevant lines covered (70.05%)

0.7 hits per line

Source File
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0.0

/src/main/java/org/commonwl/view/Scheduler.java

/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you 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.
 */

package org.commonwl.view;

import java.io.File;
import java.io.IOException;
import java.time.Duration;
import java.time.Instant;
import java.util.Calendar;
import java.util.Date;
import java.util.List;
import java.util.stream.Stream;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.filefilter.AgeFileFilter;
import org.commonwl.view.workflow.QueuedWorkflowRepository;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.scheduling.annotation.Scheduled;
import org.springframework.stereotype.Component;

/** Scheduler class for recurrent processes. */
@Component
public class Scheduler {

  private final Logger logger = LoggerFactory.getLogger(this.getClass());
  private final QueuedWorkflowRepository queuedWorkflowRepository;

  @Value("${queuedWorkflowAgeLimitHours}")
  private Integer QUEUED_WORKFLOW_AGE_LIMIT_HOURS;

  @Value("${tmpDirAgeLimitDays}")
  private Integer TMP_DIR_AGE_LIMIT_DAYS;

  // We do not want to remove the bundles, as we use the disk as a sort of
  // cache. Whenever a workflow page is displayed in the browser the UI
  // fires a request to re-generate it. We skip that by keeping files on disk.
  @Value("${graphvizStorage}")
  private String graphvizStorage;

  @Value("${gitStorage}")
  private String gitStorage;

  @Autowired
  public Scheduler(QueuedWorkflowRepository queuedWorkflowRepository) {
    this.queuedWorkflowRepository = queuedWorkflowRepository;
  }

  /**
   * A Scheduled function to delete old queued workflow entries from the queue. Age is determined by
   * QUEUED_WORKFLOW_AGE_LIMIT_HOURS
   */
  @Scheduled(cron = "${cron.deleteOldQueuedWorkflows}")
  public void removeOldQueuedWorkflowEntries() {
    Calendar calendar = Calendar.getInstance();
    Date now = new Date();
    calendar.setTime(now);

    if (QUEUED_WORKFLOW_AGE_LIMIT_HOURS == null) {
      QUEUED_WORKFLOW_AGE_LIMIT_HOURS = 24;
    }

    // calculate time QUEUED_WORKFLOW_AGE_LIMIT_HOURS before now
    calendar.add(Calendar.HOUR, -QUEUED_WORKFLOW_AGE_LIMIT_HOURS);
    Date removeTime = calendar.getTime();

    logger.info("The time is {}", now);
    logger.info("Delete time interval is : OLDER THAN {} HOURS", QUEUED_WORKFLOW_AGE_LIMIT_HOURS);
    logger.info("Deleting queued workflows older than or equal to {}", removeTime);

    logger.info(
        "{} Old queued workflows removed",
        queuedWorkflowRepository.deleteByTempRepresentation_RetrievedOnLessThanEqual(removeTime));
  }

  /**
   * Scheduled function to delete old temporary directories.
   *
   * <p>Will scan each temporary directory (graphviz, RO, git), searching for files exceeding a
   * specified threshold.
   *
   * <p>It scans the first level directories, i.e. it does not recursively scan directories. So it
   * will delete any RO or Git repository directories that exceed the threshold. Similarly, it will
   * delete any graph (svg, png, etc.) that also exceeds it.
   *
   * <p>Errors logged through Logger. Settings in Spring application properties file.
   *
   * @since 1.4.6
   */
  @Scheduled(cron = "${cron.clearTmpDir}")
  public void clearTmpDir() {
    // Temporary files used for graphviz, RO, and git may be stored in different
    // locations, so we will collect all of them here.
    List<String> temporaryDirectories = Stream.of(graphvizStorage, gitStorage).distinct().toList();
    temporaryDirectories.forEach(this::clearDirectory);
  }

  /**
   * For a given temporary directory, scans it (not recursively) for files and directories exceeding
   * the age limit threshold.
   *
   * @since 1.4.6
   * @see <a
   *     href="https://commons.apache.org/proper/commons-io/apidocs/org/apache/commons/io/filefilter/AgeFileFilter.html">https://commons.apache.org/proper/commons-io/apidocs/org/apache/commons/io/filefilter/AgeFileFilter.html</a>
   * @param temporaryDirectory temporary directory
   */
  private void clearDirectory(String temporaryDirectory) {
    final Instant cutoff = Instant.now().minus(Duration.ofDays(TMP_DIR_AGE_LIMIT_DAYS));

    File temporaryDirectoryFile = new File(temporaryDirectory);
    String[] files = temporaryDirectoryFile.list(new AgeFileFilter(Date.from(cutoff)));

    if (files != null) {
      for (String fileName : files) {
        File fileToDelete = new File(temporaryDirectoryFile, fileName);
        try {
          FileUtils.forceDelete(fileToDelete);
        } catch (IOException e) {
          // Here we probably have a more serious case. Since the Git repository, RO directory, or
          // graphs are
          // not expected to be in use, and the application must have access, I/O errors are not
          // expected and
          // must be treated as errors.
          logger.error(
              "Failed to delete old temporary file or directory [{}]: {}",
              fileToDelete.getAbsolutePath(),
              e.getMessage(),
              e);
        }
      }
    }
  }
}

1	/*
2	* Licensed to the Apache Software Foundation (ASF) under one
3	* or more contributor license agreements. See the NOTICE file
4	* distributed with this work for additional information
5	* regarding copyright ownership. The ASF licenses this file
6	* to you under the Apache License, Version 2.0 (the
7	* "License"); you may not use this file except in compliance
8	* with the License. You may obtain a copy of the License at
9	*
10	* http://www.apache.org/licenses/LICENSE-2.0
11	*
12	* Unless required by applicable law or agreed to in writing,
13	* software distributed under the License is distributed on an
14	* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
15	* KIND, either express or implied. See the License for the
16	* specific language governing permissions and limitations
17	* under the License.
18	*/
19
20	package org.commonwl.view;
21
22	import java.io.File;
23	import java.io.IOException;
24	import java.time.Duration;
25	import java.time.Instant;
26	import java.util.Calendar;
27	import java.util.Date;
28	import java.util.List;
29	import java.util.stream.Stream;
30	import org.apache.commons.io.FileUtils;
31	import org.apache.commons.io.filefilter.AgeFileFilter;
32	import org.commonwl.view.workflow.QueuedWorkflowRepository;
33	import org.slf4j.Logger;
34	import org.slf4j.LoggerFactory;
35	import org.springframework.beans.factory.annotation.Autowired;
36	import org.springframework.beans.factory.annotation.Value;
37	import org.springframework.scheduling.annotation.Scheduled;
38	import org.springframework.stereotype.Component;
39
40	/** Scheduler class for recurrent processes. */
41	@Component
42	public class Scheduler {
43
44	private final Logger logger = LoggerFactory.getLogger(this.getClass());	×
45	private final QueuedWorkflowRepository queuedWorkflowRepository;
46
47	@Value("${queuedWorkflowAgeLimitHours}")
48	private Integer QUEUED_WORKFLOW_AGE_LIMIT_HOURS;
49
50	@Value("${tmpDirAgeLimitDays}")
51	private Integer TMP_DIR_AGE_LIMIT_DAYS;
52
53	// We do not want to remove the bundles, as we use the disk as a sort of
54	// cache. Whenever a workflow page is displayed in the browser the UI
55	// fires a request to re-generate it. We skip that by keeping files on disk.
56	@Value("${graphvizStorage}")
57	private String graphvizStorage;
58
59	@Value("${gitStorage}")
60	private String gitStorage;
61
62	@Autowired
63	public Scheduler(QueuedWorkflowRepository queuedWorkflowRepository) {	×
64	this.queuedWorkflowRepository = queuedWorkflowRepository;	×
65	}	×
66
67	/**
68	* A Scheduled function to delete old queued workflow entries from the queue. Age is determined by
69	* QUEUED_WORKFLOW_AGE_LIMIT_HOURS
70	*/
71	@Scheduled(cron = "${cron.deleteOldQueuedWorkflows}")
72	public void removeOldQueuedWorkflowEntries() {
73	Calendar calendar = Calendar.getInstance();	×
74	Date now = new Date();	×
75	calendar.setTime(now);	×
76
77	if (QUEUED_WORKFLOW_AGE_LIMIT_HOURS == null) {	×
78	QUEUED_WORKFLOW_AGE_LIMIT_HOURS = 24;	×
79	}
80
81	// calculate time QUEUED_WORKFLOW_AGE_LIMIT_HOURS before now
82	calendar.add(Calendar.HOUR, -QUEUED_WORKFLOW_AGE_LIMIT_HOURS);	×
83	Date removeTime = calendar.getTime();	×
84
NEW 85	logger.info("The time is {}", now);	×
NEW 86	logger.info("Delete time interval is : OLDER THAN {} HOURS", QUEUED_WORKFLOW_AGE_LIMIT_HOURS);	×
NEW 87	logger.info("Deleting queued workflows older than or equal to {}", removeTime);	×
88
89	logger.info(	×
90	"{} Old queued workflows removed",
NEW 91	queuedWorkflowRepository.deleteByTempRepresentation_RetrievedOnLessThanEqual(removeTime));	×
UNCOV 92	}	×
93
94	/**
95	* Scheduled function to delete old temporary directories.
96	*
97	* <p>Will scan each temporary directory (graphviz, RO, git), searching for files exceeding a
98	* specified threshold.
99	*
100	* <p>It scans the first level directories, i.e. it does not recursively scan directories. So it
101	* will delete any RO or Git repository directories that exceed the threshold. Similarly, it will
102	* delete any graph (svg, png, etc.) that also exceeds it.
103	*
104	* <p>Errors logged through Logger. Settings in Spring application properties file.
105	*
106	* @since 1.4.6
107	*/
108	@Scheduled(cron = "${cron.clearTmpDir}")
109	public void clearTmpDir() {
110	// Temporary files used for graphviz, RO, and git may be stored in different
111	// locations, so we will collect all of them here.
112	List<String> temporaryDirectories = Stream.of(graphvizStorage, gitStorage).distinct().toList();	×
113	temporaryDirectories.forEach(this::clearDirectory);	×
114	}	×
115
116	/**
117	* For a given temporary directory, scans it (not recursively) for files and directories exceeding
118	* the age limit threshold.
119	*
120	* @since 1.4.6
121	* @see <a
122	* href="https://commons.apache.org/proper/commons-io/apidocs/org/apache/commons/io/filefilter/AgeFileFilter.html">https://commons.apache.org/proper/commons-io/apidocs/org/apache/commons/io/filefilter/AgeFileFilter.html</a>
123	* @param temporaryDirectory temporary directory
124	*/
125	private void clearDirectory(String temporaryDirectory) {
126	final Instant cutoff = Instant.now().minus(Duration.ofDays(TMP_DIR_AGE_LIMIT_DAYS));	×
127
128	File temporaryDirectoryFile = new File(temporaryDirectory);	×
129	String[] files = temporaryDirectoryFile.list(new AgeFileFilter(Date.from(cutoff)));	×
130
NEW 131	if (files != null) {	×
132	for (String fileName : files) {	×
133	File fileToDelete = new File(temporaryDirectoryFile, fileName);	×
134	try {
135	FileUtils.forceDelete(fileToDelete);	×
136	} catch (IOException e) {	×
137	// Here we probably have a more serious case. Since the Git repository, RO directory, or
138	// graphs are
139	// not expected to be in use, and the application must have access, I/O errors are not
140	// expected and
141	// must be treated as errors.
142	logger.error(	×
143	"Failed to delete old temporary file or directory [{}]: {}",
NEW 144	fileToDelete.getAbsolutePath(),	×
NEW 145	e.getMessage(),	×
146	e);
147	}	×
148	}
149	}
150	}	×
151	}

common-workflow-language / cwlviewer / #1999

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